Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Background

RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for expression quantitative trait locus (eQTL) studies. However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.

Results

We simulate RNA-seq read mapping over 9.5 M common SNPs and indels, with 15.6% of variants showing biased mapping rate for reference versus non-reference reads. However, removing potentially biased RNA-seq reads from an eQTL dataset of 185 individuals has a very small effect on gene and exon quantifications and eQTL discovery. We detect only a handful of likely false positive eQTLs, and overall eQTL SNPs show no significant enrichment for high mapping bias.

Conclusion

Our results suggest that RNA-seq quantifications are generally robust against allelic mapping bias, and that this does not have a severe effect on eQTL discovery. Nevertheless, we provide our catalog of putatively biased loci to allow better controlling for mapping bias to obtain more accurate results in future RNA-seq studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0467-2) contains supplementary material, which is available to authorized users.     

Cell model of catecholaminergic polymorphic ventricular tachycardia reveals early and delayed afterdepolarizations

Background

Induced pluripotent stem cells (iPSC) provide means to study the pathophysiology of genetic disorders. Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a malignant inherited ion channel disorder predominantly caused by mutations in the cardiac ryanodine receptor (RyR2). In this study the cellular characteristics of CPVT are investigated and whether the electrophysiological features of this mutation can be mimicked using iPSC -derived cardiomyocytes (CM).

Methodology/Principal Findings

Spontaneously beating CMs were differentiated from iPSCs derived from a CPVT patient carrying a P2328S mutation in RyR2 and from two healthy controls. Calcium (Ca²⁺) cycling and electrophysiological properties were studied by Ca²⁺ imaging and patch-clamp techniques. Monophasic action potential (MAP) recordings and 24h-ECGs of CPVT-P2328S patients were analyzed for the presence of afterdepolarizations. We found defects in Ca²⁺ cycling and electrophysiology in CPVT CMs, reflecting the cardiac phenotype observed in the patients. Catecholaminergic stress led to abnormal Ca²⁺ signaling and induced arrhythmias in CPVT CMs. CPVT CMs also displayed reduced sarcoplasmic reticulum (SR) Ca²⁺ content, indicating leakage of Ca²⁺ from the SR. Patch-clamp recordings of CPVT CMs revealed both delayed afterdepolarizations (DADs) during spontaneous beating and in response to adrenaline and also early afterdepolarizations (EADs) during spontaneous beating, recapitulating the changes seen in MAP and 24h-ECG recordings of patients carrying the same mutation.

Conclusions/Significance

This cell model shows aberrant Ca²⁺ cycling characteristic of CPVT and in addition to DADs it displays EADs. This cell model for CPVT provides a platform to study basic pathology, to screen drugs, and to optimize drug therapy.     

Setup and dosimetry for exposure of human skin in vivo to RF-EMF at 900 MHz

The aim of this study was a dosimetrical analysis of an experimental setup used in the exposure of 10 female volunteers to GSM 900 radiation. The exposure was carried out by irradiating a small region of the right forearms of the volunteers for 1 h, after which biopsies were taken from the exposed skin for protein analysis. The source of irradiation was a half-wave dipole fed with a computer controlled GSM phone. The specific absorption rate (SAR) induced in the skin biopsy was assessed by computer simulations. The numerical model of the arm consisted of a muscle tissue simulating cylinder covered with thin skin (1 mm) and fat (3 mm) layers. The simulation models were validated by measurements with a homogeneous cylindrical liquid phantom. The average SAR value in the biopsy was 1.3 W/kg and the estimated uncertainty +/-20% (K = 2). The main source of error was found to be variations in the distance of the forearm from the dipole (10 +/- 1 mm). Other significant sources of uncertainty are individual variations of the fat layer and arm thicknesses, and the uncertainty of radio frequency (RF) power measurement.     

Age-Related Features of Cataractogenesis in Salmon Fry. 2. Biochemical Features of Lens during Cataractogenesis

We studied biochemical features of the lipid and phospholipid composition and patter of fatty acid spectra in lenses of one and two year old salmons bearing cataracts. The lipid complex of lenses of diseased fish underwent significant changes. Cataractogenesis was accompanied by enhanced free radical oxidation and accumulation of malone dialdehyde in lenses of salmons of various ages. The intensification of oxidative processes was synchronized with the decreased level of antioxidant protection (reduced glutathione, vitamins A and E). The activity of Ca²⁺-dependent proteolytic enzymes in lenses was determined and its decrease in the case of cataract was shown.     

Effects of blood flow on lung ACE kinetics: evidence for microvascular recruitment.

The parameter Amax/Km (product of reactant enzyme mass in perfused microvessels and the constant kcat/Km), calculated from in vivo assays of pulmonary endothelial ectoenzymes (e.g., angiotensin-converting enzyme, ACE), can provide estimates of the perfused pulmonary microvascular surface area (PMSA) in the absence of enzyme dysfunction. We examined the relationship between PMSA and pulmonary blood flow (Qb) in anesthetized rabbits placed on total heart bypass, using [3H]benzoyl-Phe-Ala-Pro (BPAP) as the ACE substrate. When Qb was increased from 250 to 1,100 ml/min, at zone 3 conditions, pulmonary arterial pressure increased, pulmonary vascular resistance (PVR) decreased, and Amax/Km increased linearly, reflecting increasing PMSA. When only the left lung was perfused, increasing Qb from 250 to 636 +/- 17 ml/min (the last value representing fully recruited and/or distended vascular bed), PVR decreased, while Amax/Km increased. When Qb was further increased to 791 +/- 44 ml/min, both PVR and Amax/Km remained unchanged, confirming the lack of additional changes in PMSA. We conclude that Amax/Km provides a sensitive indication of PMSA, because it 1) increases with increasing Qb and decreasing PVR, 2) reaches a maximum at Qb values that correspond to the minimal values in PVR, and 3) like PVR, did not change with further increases in Qb. Compared with predicted changes in PMSA produced by either microvascular recruitment alone or distension alone, our data indicate that recruitment is a larger contributor to the observed increase in PMSA.     

Growth pattern of the human promyelocytic leukaemia cell line HL60

Abstract. In order to characterize the growth pattern of the human promyelocytic leukaemia cell line HL60, its kinetic parameters were studied. The doubling time was calculated from serial cell counts, the duration of the various cell cycle phases from the analysis of the labelled mitoses curve, and quiescent population from continuous labelling experiments. Proliferation in culture was exponential up to a saturation density of about 3.0 × 10⁶ cells/ml, with a doubling time of 34.0 hr. The cell cycle duration was 24.3 ± 4.1 hr (SD), and that of the cell cycle phases was: G₁, 3.8 ± 2.2 hr; S, 15.1 ± 3 hr; and G₂, 5.4 ± 1.2 hr. The growth fraction was 0.85, and cell loss was restricted to the quiescent cells. The HL60 cell line, with fully characterized kinetics, provides a useful tool for the in vitro study of substances which may affect human leukaemic myelopoietic proliferation.     

The effect of temperature on growth,indole alkaloid accumulation and lipid composition of Catharanthus roseus cell suspension cultures

Cell suspension cultures of Catharanthus roseus were used to study the effect of temperature on plant cell lipids and indole alkaloid accumulation. Lowering the cultivation temperature increased the total fatty acid content per cell dry weight relative to that at higher temperatures, mainly because of increased accumulation of unsaturated C18 acids. In addition, an increase in the relative proportion of phosphatidylcholine and phosphatidylethanolamine was observed. Within individual lipids, the degree of unsaturation was increased and the mean fatty acid chain length decreased with reducing temperature. These changes may be interpreted as modifying the cell membrane fluidity to keep it optimal for growth and metabolism at each temperature. In spite of membrane modifications, the indole alkaloid content of the cells or the medium was not affected by temperature change.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - PC phosphatidylcholine - PE phosphatidylethanolamine - PI phosphatidylinositol - PS phosphatidylserine - PG phosphatidylglycerol - CL cardiolipin - DGD digalactosyldiglyceride - MGD monogalactosyldiglyceride - NL neutral lipids - DU degree of fatty acid unsaturation - TLC thin-layer chromatography - FID-GC flame ionisation detector-gas chromatography - dw dry weight     

The effect of temperature on hairy root cultures of Catharanthus roseus: Growth,indole alkaloid accumulation and membrane lipid composition

Cultivation of Catharanthus roseus hairy root cultures at different temperatures was found to have an effect on growth rate and indole alkaloid content as well as lipid composition. When lowering the temperature, the roots responded by increasing the degree of unsaturation of cellular lipids, which was mainly due to an increased proportion of linolenic acid in the main lipid classes. The modifications in lipid composition were obviously necessary for the roots to retain the proper cell membrane fluidity at each temperature. Despite of changes in membrane lipids, no effect on the distribution of indole alkaloids between the roots and the medium could be detected. Instead, the level of alkaloid accumulation showed a clear increase with lowering temperature.Abbreviations PC phosphatidylcholine - PE phosphatidylethanolamine - PI phosphatidylinositol - PS phosphatidylserine - PG phosphatidylglycerol - CL cardiolipin - DGD digalactosyldiglyceride - MGD monogalactosyldiglyceride - NL neutral lipids - DU degree of fatty acid unsaturation     

Monte Carlo simulation of malignant growth. Examples of the behavior of chloroleukemia after specific perturbations

This paper describes a stochastic model of cell population growth constructed to simulate biological reality in different experimental conditions. Using the computer program developed, the behavior of the cell population and of several experimentally measurable kinetic parameters was studied after specific perturbations, especially those involving sudden changes in the duration of the G₁ phase of the cell cycle (chalone action). It was demonstrated that mere prolongation of the G₁ phase can lead to tumor regression. The results also showed that it is sometimes difficult, if not impossible, intuitively to reach a correct interpretation of seemingly unequivocal biological data and, hence, that conclusions regarding cell population kinetics are hazardous without the aid of a rigorous model.